@datagrok-libraries/bio 5.53.2 → 5.53.4

package/CHANGELOG.md

@@ -1,5 +1,10 @@
 # bio changelog
 
+## 5.53.3 (2025-06-02)
+
+* MSA header tracks
+* Faster methods for getting regions from ISeqSplitted
+
 ## 5.52.0 (2025-05-12)
 
 Sequence rendering with shift configuration. MSA improvements

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.53.2",
+  "version": "5.53.4",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

package/src/utils/composition-table.d.ts

@@ -0,0 +1,6 @@
+import { IMonomerLibBase } from './../types';
+import { HelmType } from './../helm/types';
+export declare function buildCompositionTable(counts: {
+    [m: string]: number;
+}, biotype: HelmType, monomerLib: IMonomerLibBase): HTMLTableElement;
+//# sourceMappingURL=composition-table.d.ts.map

package/src/utils/composition-table.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,YAAY,CAAC;AAC3C,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAEzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,GAC9E,gBAAgB,CA0ClB"}

package/src/utils/composition-table.js

@@ -0,0 +1,46 @@
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import { GAP_SYMBOL } from './macromolecule/consts';
+export function buildCompositionTable(counts, biotype, monomerLib) {
+    let sumValue = 0;
+    let maxValue = null;
+    for (const value of Object.values(counts)) {
+        sumValue = sumValue + value;
+        maxValue = maxValue === null ? value : Math.max(maxValue, value);
+    }
+    const maxRatio = maxValue / sumValue;
+    const elMap = Object.assign({}, ...Array.from(Object.entries(counts))
+        .sort((a, b) => b[1] - a[1])
+        .map(([cm, value]) => {
+        const ratio = value / sumValue;
+        let color;
+        try {
+            const colors = monomerLib.getMonomerColors(biotype, cm);
+            color = colors?.backgroundcolor || '#CCCCCC';
+        }
+        catch (error) {
+            console.warn(`Failed to get colors for monomer ${cm}:`, error);
+            color = '#CCCCCC';
+        }
+        const barDiv = ui.div('', { classes: 'macromolecule-cell-comp-analysis-bar' });
+        barDiv.style.width = `${50 * ratio / maxRatio}px`;
+        barDiv.style.backgroundColor = color;
+        if (GAP_SYMBOL === cm) {
+            barDiv.style.borderWidth = '1px';
+            barDiv.style.borderStyle = 'solid';
+            barDiv.style.borderColor = DG.Color.toHtml(DG.Color.lightGray);
+        }
+        const displayMonomer = GAP_SYMBOL === cm ? '-' : cm;
+        const valueDiv = ui.div(`${(100 * ratio).toFixed(2)}%`);
+        const el = ui.div([barDiv, valueDiv], { classes: 'macromolecule-cell-comp-analysis-value' });
+        return ({ [displayMonomer]: el });
+    }));
+    const table = ui.tableFromMap(elMap);
+    Array.from(table.rows).forEach((row) => {
+        const barCol = row.getElementsByClassName('macromolecule-cell-comp-analysis-bar')[0]
+            .style.backgroundColor;
+        row.cells[0].style.color = barCol;
+    });
+    return table;
+}
+//# sourceMappingURL=composition-table.js.map

package/src/utils/composition-table.js.map

@@ -0,0 +1 @@
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package/src/utils/macromolecule/types.d.ts

@@ -9,6 +9,11 @@ export interface ISeqSplitted {
     /** For fasta and Helm must not be enclosed to square brackets [meA].*/
     getOriginal(posIdx: number): string;
     length: number;
+    /** Returns list of canonical monomers in the region specified */
+    getCanonicalRegion(start: number, end: number): string[];
+    /** Returns the list of original monomers in the region specified */
+    getOriginalRegion(start: number, end: number): string[];
+    get gapOriginal(): string;
 }
 export interface INotationProvider {
     get defaultGapOriginal(): string;

package/src/utils/macromolecule/types.d.ts.map

@@ -1 +1 @@
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package/src/utils/macromolecule/types.js.map

@@ -1 +1 @@
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package/src/utils/macromolecule/utils.d.ts

@@ -11,6 +11,9 @@ export declare class StringListSeqSplitted implements ISeqSplitted {
     /** @param {number} posIdx monomer position 0-based index */
     getCanonical(posIdx: number): string;
     getOriginal(posIdx: number): string;
+    getCanonicalRegion(start: number, end: number): string[];
+    getOriginalRegion(start: number, end: number): string[];
+    get gapOriginal(): string;
     constructor(mList: SeqSplittedBase, gapOriginalMonomer: string);
 }
 export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
@@ -19,6 +22,9 @@ export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
     isGap(posIdx: number): boolean;
     getCanonical(posIdx: number): string;
     getOriginal(posIdx: number): string;
+    getCanonicalRegion(start: number, end: number): string[];
+    getOriginalRegion(start: number, end: number): string[];
+    get gapOriginal(): string;
     constructor(seqS: string);
 }
 /** Stats of sequences with specified splitter func, returns { freq, sameLength }.

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package/src/utils/macromolecule/utils.js

@@ -26,6 +26,22 @@ export class StringListSeqSplitted {
             throw new Error('Index out of bounds');
         return this.mList[posIdx];
     }
+    getCanonicalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        const len = actEnd - actStart;
+        const gap = this.gapOriginalMonomer;
+        return new Array(len).fill(null).map((_, i) => { const om = this.mList[i + actStart]; return om === gap ? GAP_SYMBOL : om; });
+    }
+    getOriginalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        const len = actEnd - actStart;
+        return new Array(len).fill(null).map((_, i) => this.mList[i + actStart]);
+    }
+    get gapOriginal() {
+        return this.gapOriginalMonomer;
+    }
     constructor(mList, gapOriginalMonomer) {
         this.mList = mList;
         this.gapOriginalMonomer = gapOriginalMonomer;
@@ -48,6 +64,24 @@ export class FastaSimpleSeqSplitted {
             throw new Error('Index out of bounds');
         return this.seqS[posIdx];
     }
+    getCanonicalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        const len = actEnd - actStart;
+        const gap = GapOriginals[NOTATION.FASTA];
+        return new Array(len).fill(null).map((_, i) => {
+            const om = this.seqS[i + actStart];
+            return om === gap ? GAP_SYMBOL : om;
+        });
+    }
+    getOriginalRegion(start, end) {
+        const actStart = Math.max(0, start);
+        const actEnd = Math.min(this.length, end);
+        return this.seqS.slice(actStart, actEnd); // hacky way but quite effective
+    }
+    get gapOriginal() {
+        return GapOriginals[NOTATION.FASTA];
+    }
     constructor(seqS) {
         this.seqS = seqS;
     }

package/src/utils/macromolecule/utils.js.map

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package/src/utils/sequence-position-scroller.d.ts

@@ -3,6 +3,10 @@
  * This module provides functionality for an interactive MSA (Multiple Sequence Alignment) header
  * with position markers, slider navigation, and position selection.
  */
+import * as DG from 'datagrok-api/dg';
+import { ISeqHandler } from './macromolecule/seq-handler';
+import { HelmType } from '../helm/types';
+import { IMonomerLib } from '../types';
 interface WindowRange {
     start: number;
     end: number;
@@ -22,27 +26,143 @@ interface MSAHeaderOptions {
     width?: number;
     height?: number;
     onPositionChange?: (position: number, range: WindowRange) => void;
+    onHeaderHeightChange?: (height: number) => void;
 }
 interface Preventable {
     preventDefault: () => void;
 }
+/**
+ * Base class for all MSA header tracks
+ */
+export declare abstract class MSAHeaderTrack {
+    protected ctx: CanvasRenderingContext2D | null;
+    protected visible: boolean;
+    protected height: number;
+    protected minHeight: number;
+    protected defaultHeight: number;
+    protected title: string;
+    protected tooltipEnabled: boolean;
+    protected tooltipContent: ((position: number, monomer: string | null, data: Map<string, number>) => HTMLElement) | null;
+    constructor(height?: number, minHeight?: number, title?: string);
+    /**
+     * Initialize the track with a canvas context
+     */
+    init(ctx: CanvasRenderingContext2D): void;
+    getMonomerAt(_x: number, _y: number, _position: number): string | null;
+    enableTooltip(enabled: boolean): void;
+    setTooltipContentGenerator(contentGenerator: (position: number, monomer: string | null, data: Map<string, number>) => HTMLElement): void;
+    getTooltipContent(position: number, monomer: string | null): HTMLElement | null;
+    /**
+     * Get data for a specific position (to be implemented by subclasses)
+     */
+    protected getPositionData(position: number): Map<string, number> | null;
+    setVisible(visible: boolean): void;
+    getHeight(): number;
+    getDefaultHeight(): number;
+    getMinHeight(): number;
+    setHeight(height: number): void;
+    resetHeight(): void;
+    isVisible(): boolean;
+    setTitle(title: string): void;
+    getTitle(): string;
+    /**
+     * Draw the track at the specified position
+     */
+    abstract draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, currentPosition: number): void;
+}
+export declare class WebLogoTrack extends MSAHeaderTrack {
+    private data;
+    private monomerLib;
+    private biotype;
+    private hoveredPosition;
+    private hoveredMonomer;
+    constructor(data?: Map<number, Map<string, number>>, height?: number, _colorScheme?: string, title?: string);
+    setHovered(position: number, monomer: string | null): void;
+    protected getPositionData(position: number): Map<string, number> | null;
+    setupDefaultTooltip(): void;
+    private createFrequencyTable;
+    private createTooltipContent;
+    setMonomerLib(monomerLib: IMonomerLib): void;
+    setBiotype(biotype: HelmType): void;
+    /**
+     * Calculate which monomer is at the specified coordinates within a WebLogo column
+     */
+    getMonomerAt(x: number, y: number, position: number): string | null;
+    updateData(data: Map<number, Map<string, number>>): void;
+    /**
+     * Draw the WebLogo track
+     */
+    draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, currentPosition: number): void;
+    private drawWebLogoColumn;
+    private drawLettersInColumn;
+    private drawColumnBorder;
+    private drawLetter;
+    private drawLetterSeparators;
+    private drawLetterText;
+    private getMonomerBackgroundColor;
+    private getMonomerTextColor;
+}
+/**
+ * Track for displaying conservation bars
+ */
+export declare class ConservationTrack extends MSAHeaderTrack {
+    private data;
+    private colorScheme;
+    constructor(data: number[], height?: number, colorScheme?: 'default' | 'rainbow' | 'heatmap', title?: string);
+    updateData(data: number[]): void;
+    /**
+     * Draw the conservation track
+     */
+    draw(x: number, y: number, width: number, height: number, windowStart: number, positionWidth: number, totalPositions: number, currentPosition: number): void;
+    private drawConservationBar;
+}
 export declare class MSAScrollingHeader {
     private config;
     private state;
     private canvas;
     private ctx;
     private eventElement;
+    private tracks;
+    private currentHoverPosition;
+    private currentHoverTrack;
+    private currentHoverMonomer;
+    private previousHoverPosition;
+    private previousHoverTrack;
+    private previousHoverMonomer;
+    private dataFrame;
+    private seqHandler;
+    private seqColumn;
+    private onSelectionCallback;
+    private trackButtons;
+    private userSelectedTracks;
+    constructor(options: MSAHeaderOptions);
+    private determineVisibleTracks;
+    private drawTrackButtons;
+    private drawTrackButton;
+    private handleTrackButtonClick;
+    private snapToTrackHeight;
+    private resetToAutoMode;
     /**
-     * Constructor for the MSA Header
-     * @param {MSAHeaderOptions} options - Configuration options
+     * Draw the column title (shown when above threshold)
      */
-    constructor(options: MSAHeaderOptions);
+    private drawColumnTitle;
+    private clearHoverStates;
+    private redraw;
+    setSelectionData(dataFrame: DG.DataFrame, seqColumn: DG.Column<string>, seqHandler: ISeqHandler, callback?: (position: number, monomer: string) => void): void;
+    setupTooltipHandling(): void;
+    private handleTooltipMouseMove;
+    private handleTooltipMouseLeave;
+    private hideTooltip;
+    draw(x: number, y: number, w: number, h: number, currentPos: number, scrollerStart: number, preventable: Preventable, columnName?: string): void;
     /**
-     * Initialize the component
+     * Draw the dotted cells area with position markers
      */
-    private init;
-    get isValid(): boolean;
-    draw(x: number, y: number, w: number, h: number, currentPos: number, scrollerStart: number, preventable: Preventable): void;
+    private drawDottedCells;
+    /**
+     * Draw the position slider
+     */
+    private drawSlider;
+    private setupEventElement;
     getCoords(e: MouseEvent): {
         x: number;
         y: number;
@@ -53,57 +173,37 @@ export declare class MSAScrollingHeader {
     isInSliderArea(e: MouseEvent): boolean;
     get sliderWidth(): number;
     isInSliderDraggableArea(e: MouseEvent): boolean;
-    /**
-     * Handle mouse down (start dragging)
-     * @param {MouseEvent} e - Mouse event
-     */
+    private setupEventListeners;
+    private handleSelectionClick;
+    private selectRowsWithMonomerAtPosition;
+    private init;
+    addTrack(id: string, track: MSAHeaderTrack): void;
+    removeTrack(id: string): void;
+    getTrack<T extends MSAHeaderTrack>(id: string): T | undefined;
+    updateTrack<T extends MSAHeaderTrack>(id: string, updater: (track: T) => void): void;
+    get isValid(): boolean;
     private handleMouseDown;
     private handleMouseWheel;
-    /**
-     * Handle mouse move (dragging)
-     * @param {MouseEvent} e - Mouse event
-     */
     private handleMouseMove;
     private handleKeyDown;
-    /**
-     * Handle mouse up (end dragging)
-     */
     private handleMouseUp;
-    /**
-     * Handle slider drag
-     * @param {number} x - X position of mouse
-     */
     private handleSliderDrag;
     get headerHeight(): number;
-    /** Soft setting of header hight, without redrawing or update event
-     * @param {number} value - New header height
-     */
     set headerHeight(value: number);
-    /**
-     * Handle click on positions
-     * @param {MouseEvent} e - Mouse event
-     */
     private handleClick;
-    /**
-     * Get the current window range
-     * @return {WindowRange} Object with start and end properties
-     */
     getWindowRange(): WindowRange;
-    /**
-     * Update configuration
-     * @param {MSAHeaderOptions} newConfig - New configuration options
-     */
     updateConfig(newConfig: Partial<MSAHeaderOptions>): void;
-    /**
-     * Get current position
-     * @return {number} Current position
-     */
     getCurrentPosition(): number;
+    setCurrentPosition(position: number): void;
     /**
-     * Set current position
-     * @param {number} position - New position
+     * ADDED: Public methods for external control
      */
-    setCurrentPosition(position: number): void;
+    getHeightThresholds(): {
+        BASE: number;
+        WITH_TITLE: number;
+        WITH_WEBLOGO: number;
+        WITH_BOTH: number;
+    };
 }
 export {};
 //# sourceMappingURL=sequence-position-scroller.d.ts.map

package/src/utils/sequence-position-scroller.d.ts.map

@@ -1 +1 @@
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